Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/c1e672436837a82efe1a6e68027914/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/1c8fe6a6930ebbd9aaee7ba7e2cb3f/dna_s761.SJ.out.tab
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/1c8fe6a6930ebbd9aaee7ba7e2cb3f/dna_s761.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/1c8fe6a6930ebbd9aaee7ba7e2cb3f/dna_s761.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/c1e672436837a82efe1a6e68027914/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/e4c7c021d8ea70669d08e158ca96c5/dna_s761.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (7 inputs)

07:58:21 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes

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[3510000], rate=19145454.55/min 07:58:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file dna_s761.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > dna_s761.cancer.introns.prelim 
Use of uninitialized value $ctat_genome_lib in concatenation (.) or string at /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl line 18.
-dna_s761.introns: identified 16 cancer introns
07:58:38 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file dna_s761.introns  --ctat_genome_lib ctat_genome_lib_build_dir  --intron_col 0  > dna_s761.cancer.introns.prelim 
07:58:38 : INFO : Running: touch /tmp/nxf.98JhhqVM4p/dna_s761.chckpts/prelim_introns.ok
07:58:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates dna_s761.cancer.introns.prelim --min_total_reads 5  > dna_s761.cancer.introns 
07:58:38 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates dna_s761.cancer.introns.prelim --min_total_reads 5  > dna_s761.cancer.introns 
07:58:38 : INFO : Running: touch /tmp/nxf.98JhhqVM4p/dna_s761.chckpts/introns_filtered.ok
07:58:38 : INFO : -found 4 cancer introns
07:58:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns dna_s761.introns  --cancer_introns dna_s761.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed dna_s761.introns.for_IGV.bed 
07:58:38 : INFO :  Creating the BED File.
07:58:38 : INFO : Saving Bed File as dna_s761.introns.for_IGV.bed
07:58:38 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns dna_s761.introns  --cancer_introns dna_s761.cancer.introns  --genome_lib_dir ctat_genome_lib_build_dir  --output_bed dna_s761.introns.for_IGV.bed 
07:58:38 : INFO : Running: touch /tmp/nxf.98JhhqVM4p/dna_s761.chckpts/intron_igv_bed.ok
07:58:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed dna_s761.introns.for_IGV.bed  --bam dna_s761.Aligned.sortedByCoord.out.bam  --output_prefix dna_s761 
[W::hts_idx_load3] The index file is older than the data file: dna_s761.Aligned.sortedByCoord.out.bam.bai
07:58:39 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed dna_s761.introns.for_IGV.bed  --bam dna_s761.Aligned.sortedByCoord.out.bam  --output_prefix dna_s761 
07:58:39 : INFO : Running: touch /tmp/nxf.98JhhqVM4p/dna_s761.chckpts/reads_alignments_extracted.ok
07:58:39 : INFO : Running: samtools sort -o dna_s761.cancer_intron_reads.sorted.bam dna_s761.cancer_intron_reads.bam
07:58:39 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o dna_s761.cancer_intron_reads.sorted.bam dna_s761.cancer_intron_reads.bam
07:58:39 : INFO : Running: touch /tmp/nxf.98JhhqVM4p/dna_s761.chckpts/sort_cancer_intron_reads.ok
07:58:39 : INFO : Running: samtools sort -o dna_s761.gene_reads.sorted.bam dna_s761.gene_reads.bam
07:58:40 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o dna_s761.gene_reads.sorted.bam dna_s761.gene_reads.bam
07:58:40 : INFO : Running: touch /tmp/nxf.98JhhqVM4p/dna_s761.chckpts/sort_gene_reads.ok
07:58:40 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o dna_s761.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  dna_s761.gene_reads.sorted.bam 
Done with chr chr1.
Done with chr chr4.
Done with chr chr11.
Done with chr chr12.
07:58:40 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50  -i 50  -o dna_s761.gene_reads.sorted.sifted.bam.tmp  --keep_secondary  dna_s761.gene_reads.sorted.bam 
07:58:40 : INFO : Running: touch /tmp/nxf.98JhhqVM4p/dna_s761.chckpts/dna_s761.gene_reads.sorted.sifted.bam.tmp.ok
07:58:40 : INFO : Running: samtools sort -o dna_s761.gene_reads.sorted.sifted.bam dna_s761.gene_reads.sorted.sifted.bam.tmp
07:58:41 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o dna_s761.gene_reads.sorted.sifted.bam dna_s761.gene_reads.sorted.sifted.bam.tmp
07:58:41 : INFO : Running: touch /tmp/nxf.98JhhqVM4p/dna_s761.chckpts/dna_s761.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:58:41 : INFO : Running: samtools index dna_s761.gene_reads.sorted.sifted.bam 
07:58:41 : INFO : Execution Time = 0.00 minutes. CMD: samtools index dna_s761.gene_reads.sorted.sifted.bam 
07:58:41 : INFO : Running: touch /tmp/nxf.98JhhqVM4p/dna_s761.chckpts/dna_s761.gene_reads.sorted.sifted.bam.indexed.ok
07:58:41 : INFO : Running: samtools index dna_s761.cancer_intron_reads.sorted.bam 
07:58:41 : INFO : Execution Time = 0.00 minutes. CMD: samtools index dna_s761.cancer_intron_reads.sorted.bam 
07:58:41 : INFO : Running: touch /tmp/nxf.98JhhqVM4p/dna_s761.chckpts/dna_s761.cancer_intron_reads.sorted.bam.indexed.ok
07:58:41 : INFO : Running: create_report dna_s761.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output dna_s761.ctat-splicing.igv.html  --track-config dna_s761.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: dna_s761' 
07:58:41 : INFO : Execution Time = 0.01 minutes. CMD: create_report dna_s761.introns.for_IGV.bed  ctat_genome_lib_build_dir/ref_genome.fa  --type junction  --output dna_s761.ctat-splicing.igv.html  --track-config dna_s761.igv.tracks  --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx  --title 'CTAT_Splicing: dna_s761' 
07:58:41 : INFO : Running: touch /tmp/nxf.98JhhqVM4p/dna_s761.chckpts/igv_create_html.ok
07:58:41 : INFO : done.